Hi David,
Thanks for these tips...I will definitely keep these in mind...
Though, I have a really silly question but...since my production run is
carried out ns by ns...I am wondering if it is possible that iwrap=1 could
be turned off in later runs....? Would it affect the simulation
integrity......? If not I could just re-run last part of the simulation...
(I did think about that if only I didn't specify iwrap=1.....!!!)
This problem gives me a deeper understanding on periodic system and
trajectory simulation...
-Guqin
On Tue, Jul 11, 2017 at 1:16 PM, David Case <david.case.rutgers.edu> wrote:
> On Tue, Jul 11, 2017, Dan Roe wrote:
>
> > Wow - this is certainly a challenging system to image! No one molecule
> > can be considered "center" - in fact, there isn't even a region of a
> > molecule that can be considered to be the center since when the
> > hexamer is formed there is a large empty space in the center (from
> > looking at the system this appears to be the way it should be
> > assembled).
>
> I can't offer much help now, but will take this opportunity to offer
> some cautionary advice for future simulations:
>
> 1. Always use ioutfm=1 (the default, except in rather old versions of
> Amber)
>
> 2. Avoid using iwrap=1 for anything involving much more than
> a monomer (or perhaps dimer) and mobile water and ions.
>
> [If you are worried about precision loss because of not wrapping on the
> fly,
> center and autoimage a restart file occasionally. Check visually that
> the imaging "worked", then used the revised restart file to continue the
> simulation.]
>
> 3. Use a big enough box. For a large box, it's easier to figure out how
> to pack everything together into a single unit cell than for a smaller
> one.
>
> ...dac
>
> p.s.: I actually think point 2 above should be "don't use iwrap=1, period."
> But I'm open to counterarguments.
>
>
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>
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Tue Jul 11 2017 - 11:00:02 PDT
